Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

• Published in: Molecular cell Vol. 73; no. 4; pp. 815 - 829.e7
• Main Authors: Guo, Lin, Lin, Lihui, Wang, Xiaoshan, Gao, Mingwei, Cao, Shangtao, Mai, Yuanbang, Wu, Fang, Kuang, Junqi, Liu, He, Yang, Jiaqi, Chu, Shilong, Song, Hong, Li, Dongwei, Liu, Yujian, Wu, Kaixin, Liu, Jiadong, Wang, Jinyong, Pan, Guangjin, Hutchins, Andrew P., Liu, Jing, Pei, Duanqing, Chen, Jiekai
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.02.2019
• Subjects: bifurcation; cell fate decision; Dppa5a; induced pluripotent stem cells; Interferon gamma; keratinocytes; Klf4; Oct4; reprogramming; sequence analysis; single-cell RNA sequencing; somatic cells; Sox2; reprogramming; single-cell RNA sequencing; Dppa5a; Oct4; Sox2; bifurcation; cell fate decision; induced pluripotent stem cells; Klf4; Interferon gamma
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2019.01.042

Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs), which is a highly heterogeneous process. Here we report the cell fate continuum during somatic cell reprogramming at single-cell resolution. We first develop SOT to analyze cell fate continuum from Oct4/Sox2/Klf4- or OSK-mediated reprogramming and show that cells bifurcate into two categories, reprogramming potential (RP) or non-reprogramming (NR). We further show that Klf4 contributes to Cd34+/Fxyd5+/Psca+ keratinocyte-like NR fate and that IFN-γ impedes the final transition to chimera-competent pluripotency along the RP cells. We analyze more than 150,000 single cells from both OSK and chemical reprograming and identify additional NR/RP bifurcation points. Our work reveals a generic bifurcation model for cell fate decisions during somatic cell reprogramming that may be applicable to other systems and inspire further improvements for reprogramming. [Display omitted] •Cell fate continuum generated by somatic reprogramming•Single-cell Orientation Tracing (SOT) for fate trajectory detection•Two non-reprogramming trajectories regulated by Klf4 and IFN-γ•A generic bifurcation model for cell fate decisions Guo et al. report the cell fate continuum during induced pluripotent stem cell (iPSC) reprogramming at single-cell resolution. By developing SOT as a new analytic tool, they identify several previously unknown bifurcation points along the reprogramming path and propose a generic bifurcation model for cell fate decisions.